Human Gene DARS2 (ENST00000649689.2_6) from GENCODE V47lift37
  Description: aspartyl-tRNA synthetase 2, mitochondrial, transcript variant 1 (from RefSeq NM_018122.5)
Gencode Transcript: ENST00000649689.2_6
Gencode Gene: ENSG00000117593.12_11
Transcript (Including UTRs)
   Position: hg19 chr1:173,793,811-173,827,684 Size: 33,874 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr1:173,794,368-173,826,843 Size: 32,476 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:173,793,811-173,827,684)mRNA (may differ from genome)Protein (645 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYDM_HUMAN
DESCRIPTION: RecName: Full=Aspartate--tRNA ligase, mitochondrial; EC=6.1.1.12; AltName: Full=Aspartyl-tRNA synthetase; Short=AspRS; Flags: Precursor;
CATALYTIC ACTIVITY: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Mitochondrion matrix.
DISEASE: Defects in DARS2 are a cause of leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) [MIM:611105]. LBSL is an autosomal recessive disease and is defined on the basis of a highly characteristic constellation of abnormalities observed by magnetic resonance imaging and spectroscopy. Affected individuals develop slowly progressive cerebellar ataxia, spasticity, and dorsal column dysfunction, sometimes with a mild cognitive deficit or decline.
SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/DARS2";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DARS2
Diseases sorted by gene-association score: leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation* (1669), 3-methylglutaconic aciduria, type v (7), autosomal recessive disease (6), myoclonic epilepsy associated with ragged-red fibers (4), cerebellar ataxia (2), mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -181.70557-0.326 Picture PostScript Text
3' UTR -184.30841-0.219 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004364 - aa-tRNA-synt_II
IPR018150 - aa-tRNA-synt_II-like
IPR006195 - aa-tRNA-synth_II
IPR004524 - Asp-tRNA-ligase_IIb_bac/mt
IPR002312 - Asp/Asn-tRNA-synth_IIb
IPR004115 - GAD_dom
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR004365 - NA-bd_OB_tRNA-helicase

Pfam Domains:
PF00152 - tRNA synthetases class II (D, K and N)
PF01336 - OB-fold nucleic acid binding domain
PF02938 - GAD domain

SCOP Domains:
101756 - Hypothetical protein YgiW
50249 - Nucleic acid-binding proteins
55681 - Class II aaRS and biotin synthetases
55261 - GAD domain-like

ModBase Predicted Comparative 3D Structure on Q6PI48
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004815 aspartate-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042803 protein homodimerization activity
GO:0050560 aspartate-tRNA(Asn) ligase activity

Biological Process:
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0043039 tRNA aminoacylation
GO:0070145 mitochondrial asparaginyl-tRNA aminoacylation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  BC045173 - Homo sapiens aspartyl-tRNA synthetase 2, mitochondrial, mRNA (cDNA clone MGC:43833 IMAGE:5273243), complete cds.
AL833633 - Homo sapiens mRNA; cDNA DKFZp686H0379 (from clone DKFZp686H0379).
AK290873 - Homo sapiens cDNA FLJ76156 complete cds, highly similar to Homo sapiens aspartyl-tRNA synthetase 2 (DARS2), mRNA.
CU692254 - Synthetic construct Homo sapiens gateway clone IMAGE:100020969 5' read DARS2 mRNA.
KJ894144 - Synthetic construct Homo sapiens clone ccsbBroadEn_03538 DARS2 gene, encodes complete protein.
KR710934 - Synthetic construct Homo sapiens clone CCSBHm_00018294 DARS2 (DARS2) mRNA, encodes complete protein.
KR710935 - Synthetic construct Homo sapiens clone CCSBHm_00018295 DARS2 (DARS2) mRNA, encodes complete protein.
KR710936 - Synthetic construct Homo sapiens clone CCSBHm_00018296 DARS2 (DARS2) mRNA, encodes complete protein.
KR710937 - Synthetic construct Homo sapiens clone CCSBHm_00018306 DARS2 (DARS2) mRNA, encodes complete protein.
AK022754 - Homo sapiens cDNA FLJ12692 fis, clone NT2RM4002623, weakly similar to ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12).
AK001376 - Homo sapiens cDNA FLJ10514 fis, clone NT2RP2000710, weakly similar to ASPARTYL-TRNA SYNTHETASE (EC 6.1.1.12).
JD494656 - Sequence 475680 from Patent EP1572962.
JD312661 - Sequence 293685 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
TRNA-CHARGING-PWY - tRNA charging

Reactome (by CSHL, EBI, and GO)

Protein Q6PI48 (Reactome details) participates in the following event(s):

R-HSA-380229 aspartate + tRNA(Asp) + ATP => Asp-tRNA(Asp) + AMP + pyrophosphate
R-HSA-379726 Mitochondrial tRNA aminoacylation
R-HSA-379724 tRNA Aminoacylation
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000649689.1, NM_018122, Q6PI48, SYDM_HUMAN, uc328qnx.1, uc328qnx.2
UCSC ID: ENST00000649689.2_6
RefSeq Accession: NM_018122.5
Protein: Q6PI48 (aka SYDM_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene DARS2:
lbsl (Leukoencephalopathy with Brain Stem and Spinal Cord Involvement and Lactate Elevation)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.